Question: Sva batch correction for rna seq
0
gravatar for iside
4.0 years ago by
iside10
European Union
iside10 wrote:

Dear all,

I am performing a differential expression analysis with deseq2, but I have firstly to take into account batch effects. 
I have an info file with several technical confounders and other information for the samples (twins), like family and zygosity.
As you suggested, I am using the svaseq function for correcting the batch effects, according to:
http://www.bioconductor.org/help/workflows/rnaseqGene/#batch

this is my workflow:

dds <- DESeqDataSetFromMatrix(countData = counts,
                                  colData = info,
                                  design = ~ condition)
dds<-DESeq(dds)

dat <- counts(dds, normalized=TRUE)

mod <- model.matrix(~ condition, info)
mod0 <- model.matrix(~ 1, info)
svseq <- svaseq(dat, mod, mod0, n.sv=2)

I understand that this way I will clean the dataset, but how can I take into account also the family relatedness? Can I add this information in the model (mod?) or can I do it in the following steps of the differential expression analysis? including in the model not only condition and surrogate variables (do they have to be 2?), but also family or zygosity?

design <- ~ SV1 + SV2 + fam + condition

Thanks 

Best Regards

ADD COMMENTlink modified 3.9 years ago by Biostar ♦♦ 20 • written 4.0 years ago by iside10
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